Abstract We present a study of the Ca ii K and IR triplet lines in a sample of classical T Tauri stars in the Chamaeleon I star-forming region. We study X-shooter spectra of the stars in the sample and find that in some of these stars the Ca ii lines are much weaker than expected from their H line fluxes and mass accretion rates. Since the Ca ii K lines have characteristic magnetospheric accretion line profiles and the magnetospheric flows feed directly from the inner disk, we interpret the Ca deficiency in terms of depletion due to processes happening in the disk. To test this hypothesis, we define a coarse depletion indicator using the flux of the Ca ii K line and show that it correlates with disk properties. In particular, using indicators extracted from Spitzer/IRS spectra, we obtain that all the transitional and pretransitional disks of the sample show depletion, consistent with the trapping of refractories in pressure bumps created by planets and/or in the planets themselves. We find full disks with Ca depletion in the sample that also show indications of advanced dust evolution. We apply magnetospheric accretion models to fit the Balmer and Ca ii line fluxes of a star showing clear Ca depletion and derive a Ca abundance in its inner disk of about 17% solar.